Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006710.1 Hibiscus syriacus cultivar Beakdansim tig00016725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2941931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:486 original size:14 final size:14
Alignment explanation
Indices: 463--504 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
453 AGAATATTAT
463 TTTAAATATTATT-G
1 TTTAAATATT-TTAG
*
477 TTTAAGTATTTTAG
1 TTTAAATATTTTAG
491 TTTAAATAGTTTTA
1 TTTAAATA-TTTTA
505 AGTGTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 17 0.71
15 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (14 bp):
TTTAAATATTTTAG
Found at i:1123 original size:17 final size:17
Alignment explanation
Indices: 1101--1139 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1091 CTTTAATTGC
*
1101 TATTTAATTATTTTCTT
1 TATTTAATTATTATCTT
*
1118 TATTTAATTCTTATCTT
1 TATTTAATTATTATCTT
1135 TATTT
1 TATTT
1140 TAAAAACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTAATTATTATCTT
Found at i:2720 original size:2 final size:2
Alignment explanation
Indices: 2715--2743 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2705 TATTATTTTA
2715 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2744 TGTCGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2725 original size:19 final size:19
Alignment explanation
Indices: 2701--2743 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2691 GATTTAGTTT
*
2701 TATATAT-TAT-TTTAATA
1 TATATATATATATATAATA
2718 TATATATATATATATAATA
1 TATATATATATATATAATA
2737 TATATAT
1 TATATAT
2744 TGTCGAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 3 0.13
19 13 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATATATATATATAATA
Found at i:5268 original size:24 final size:24
Alignment explanation
Indices: 5225--5270 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5215 CTATTCTTTC
* *
5225 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATCGAACTCAAATTTTAG
*
5249 GCTTCAATCGAACTCTAATTTT
1 GCTTCAATCGAACTCAAATTTT
5271 TTTTTTGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (24 bp):
GCTTCAATCGAACTCAAATTTTAG
Found at i:7973 original size:20 final size:20
Alignment explanation
Indices: 7948--8128 Score: 168
Period size: 20 Copynumber: 8.7 Consensus size: 20
7938 TTTTCCTAAT
*
7948 TCGCAATGCGAATACGTAGA
1 TCGCAATGCGAATACGTAAA
7968 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
7988 TCGCAACGCGATTAAC-TAAA
1 TCGCAATGCGAAT-ACGTAAA
* *
8008 TCGCAATGCGAATTGTGATTTTCATAAT
1 TCGCAATGCGAA---T-A----CGTAAA
*
8036 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
8056 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
*
8076 TCGCAATGCGAATTA-GGAAA
1 TCGCAATGCGAA-TACGTAAA
8096 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
8116 TCGCAATGCGAAT
1 TCGCAATGCGAAT
8129 CTGACTATCG
Statistics
Matches: 132, Mismatches: 18, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.02
20 107 0.81
21 4 0.03
23 2 0.02
24 1 0.01
25 1 0.01
27 1 0.01
28 14 0.11
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:8097 original size:88 final size:88
Alignment explanation
Indices: 7936--8108 Score: 249
Period size: 88 Copynumber: 2.0 Consensus size: 88
7926 AATTCGTTAC
* * * *
7936 GATTTTCCTAATTCGCAATGCGAATACGTAGATCGCAATGCGAATACGTAAATCGCAACGCGATT
1 GATTTTCATAATTCGCAATGCGAATACGTAAATCGCAACGCGAATAAGTAAATCGCAACGCGATT
*
8001 AACTAAATCGCAATGCGAATTGT
66 AACGAAATCGCAATGCGAATTGT
* * *
8024 GATTTTCATAATTCGCAATGTGAATACGTAAATCGCAACGCGATTAAGTAAATCGCAATGCGAAT
1 GATTTTCATAATTCGCAATGCGAATACGTAAATCGCAACGCGAATAAGTAAATCGCAACGCG-AT
*
8089 T-AGGAAATCGCAATGCGAAT
65 TAACGAAATCGCAATGCGAAT
8109 ACGTAAATCG
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
88 72 0.96
89 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (88 bp):
GATTTTCATAATTCGCAATGCGAATACGTAAATCGCAACGCGAATAAGTAAATCGCAACGCGATT
AACGAAATCGCAATGCGAATTGT
Found at i:8139 original size:40 final size:39
Alignment explanation
Indices: 8036--8146 Score: 118
Period size: 40 Copynumber: 2.8 Consensus size: 39
8026 TTTTCATAAT
* * *
8036 TCGCAATGTGAA-TACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATTA-G-AAATCGCAATGCGAATAAGTAAA
*
8076 TCGCAATGCGAATTAGGAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTA-GAAATCGCAATGCGAATAAGTAAA
*
8116 TCGCAATGCGAATCT-GACTATCGCAATGCGA
1 TCGCAATGCGAAT-TAGA-AATCGCAATGCGA
8147 TTTACATAGC
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.03
40 56 0.90
41 4 0.06
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (39 bp):
TCGCAATGCGAATTAGAAATCGCAATGCGAATAAGTAAA
Found at i:8706 original size:19 final size:21
Alignment explanation
Indices: 8659--8709 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
8649 TTTCGAGAAT
8659 AAAATCGCAACGCGGAAAAATG
1 AAAATCGCAACGCGG-AAAATG
**
8681 ACTATCGCAACGC-G-AAATG
1 AAAATCGCAACGCGGAAAATG
8700 AAAATCGCAA
1 AAAATCGCAA
8710 TGAGAGAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 13 0.52
21 1 0.04
22 11 0.44
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.12
Consensus pattern (21 bp):
AAAATCGCAACGCGGAAAATG
Found at i:8840 original size:20 final size:19
Alignment explanation
Indices: 8737--8848 Score: 119
Period size: 20 Copynumber: 6.1 Consensus size: 19
8727 GAAACCAAAA
*
8737 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
8756 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
8770 TCTCGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
**
8788 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
8807 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
8827 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
8847 TC
1 TC
8849 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.13
15 3 0.04
17 3 0.04
18 10 0.13
19 18 0.23
20 33 0.42
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:8846 original size:40 final size:38
Alignment explanation
Indices: 8742--8848 Score: 109
Period size: 32 Copynumber: 2.9 Consensus size: 38
8732 CAAAATCGCA
*
8742 TTGCGATTTTCATTTCGCGTTGCGAT--TC---T-CTCG
1 TTGCGA-TTTCATTTCGCGTTGCGATAGTCATTTCCGCG
8775 TTGCGATTTCATTTCGCGTTGCGATAGTCATTTCCGCG
1 TTGCGATTTCATTTCGCGTTGCGATAGTCATTTCCGCG
* **
8813 TTGCGATTTTCATTCTCTCGTTGCGATTTTCATTTC
1 TTGCGA-TTTCATT-TCGCGTTGCGATAGTCATTTC
8849 AACCAAAAGA
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
32 19 0.31
33 6 0.10
34 2 0.03
37 1 0.02
38 9 0.15
39 7 0.11
40 18 0.29
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (38 bp):
TTGCGATTTCATTTCGCGTTGCGATAGTCATTTCCGCG
Found at i:10905 original size:20 final size:20
Alignment explanation
Indices: 10880--11072 Score: 246
Period size: 20 Copynumber: 9.7 Consensus size: 20
10870 CGATTTAGGA
10880 AAATCGCAATGCGGTTACGT
1 AAATCGCAATGCGGTTACGT
10900 AAATCGCAATGCGGTTACGT
1 AAATCGCAATGCGGTTACGT
*
10920 AAATCGCAATGCGGTTACAT
1 AAATCGCAATGCGGTTACGT
10940 AAATCGCAATGCGGTTACGT
1 AAATCGCAATGCGGTTACGT
10960 AAATCGCAATGCGGTTACGT
1 AAATCGCAATGCGGTTACGT
** * *
10980 AAATCGCAATGCAAATTATGA
1 AAATCGCAATGC-GGTTACGT
*
11001 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGGTTACGT
* **
11021 AAATTGCAATGCGAATACGT
1 AAATCGCAATGCGGTTACGT
* *
11041 -AATCGCAATGTGATTTACGT
1 AAATCGCAATGCG-GTTACGT
*
11061 -AATCGCATTGCG
1 AAATCGCAATGCG
11073 ATTTTCCTAA
Statistics
Matches: 154, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
19 10 0.06
20 128 0.83
21 16 0.10
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (20 bp):
AAATCGCAATGCGGTTACGT
Found at i:10924 original size:40 final size:40
Alignment explanation
Indices: 10880--11115 Score: 253
Period size: 40 Copynumber: 5.9 Consensus size: 40
10870 CGATTTAGGA
*
10880 AAATCGCAATGCGGTTACGTAAATCGCAATGCGGTTACGT
1 AAATCGCAATGCGGTTACGTAAATCGCAATGCGATTACGT
* *
10920 AAATCGCAATGCGGTTACATAAATCGCAATGCGGTTACGT
1 AAATCGCAATGCGGTTACGTAAATCGCAATGCGATTACGT
* * *
10960 AAATCGCAATGCGGTTACGTAAATCGCAATGCAAATTATGA
1 AAATCGCAATGCGGTTACGTAAATCGCAATGC-GATTACGT
* * *
11001 AAATCGCAATGCGATTACGTAAATTGCAATGCGAATACGT
1 AAATCGCAATGCGGTTACGTAAATCGCAATGCGATTACGT
* * * * *
11041 -AATCGCAATGTGATTTACGT-AATCGCATTGCGATTTTCCT
1 AAATCGCAATGCG-GTTACGTAAATCGCAATGCGA-TTACGT
* * * * *
11081 AATTTGCATTGCGTTTACGT-AATCGCATTGCGATT
1 AAATCGCAATGCGGTTACGTAAATCGCAATGCGATT
11116 TTCCTAATTC
Statistics
Matches: 169, Mismatches: 23, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
39 24 0.14
40 103 0.61
41 42 0.25
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (40 bp):
AAATCGCAATGCGGTTACGTAAATCGCAATGCGATTACGT
Found at i:11075 original size:20 final size:20
Alignment explanation
Indices: 10881--11217 Score: 204
Period size: 20 Copynumber: 16.7 Consensus size: 20
10871 GATTTAGGAA
*
10881 AATCGCAATGCG-GTTACGT
1 AATCGCAATGCGATTTACGT
*
10900 AAATCGCAATGCG-GTTACGT
1 -AATCGCAATGCGATTTACGT
* *
10920 AAATCGCAATGCG-GTTACAT
1 -AATCGCAATGCGATTTACGT
*
10940 AAATCGCAATGCG-GTTACGT
1 -AATCGCAATGCGATTTACGT
*
10960 AAATCGCAATGCG-GTTACGT
1 -AATCGCAATGCGATTTACGT
* * * *
10980 AAATCGCAATGCAAATTATGAA
1 -AATCGCAATGCGATTTACG-T
11002 AATCGCAATGCGA-TTACGT
1 AATCGCAATGCGATTTACGT
* *
11021 AAATTGCAATGCGA-ATACGT
1 -AATCGCAATGCGATTTACGT
*
11041 AATCGCAATGTGATTTACGT
1 AATCGCAATGCGATTTACGT
* * *
11061 AATCGCATTGCGATTTTCCT
1 AATCGCAATGCGATTTACGT
* *
11081 AATTTGCATTGCG-TTTACGT
1 AA-TCGCAATGCGATTTACGT
* * *
11101 AATCGCATTGCGATTTTCCT
1 AATCGCAATGCGATTTACGT
*
11121 AATTCGCATTGCGATTTACGT
1 AA-TCGCAATGCGATTTACGT
* * * *
11142 AATCTCATTGTGATTTAAGT
1 AATCGCAATGCGATTTACGT
* * * * *
11162 ATTCGCATTGCGAATTAGGAA
1 AATCGCAATGCGATTTACG-T
* ** *
11183 AATCGCAACGCGAATTTGGGA
1 AATCGCAATGCG-ATTTACGT
11204 AATCGCAATGCGAT
1 AATCGCAATGCGAT
11218 AGTCAGAATC
Statistics
Matches: 267, Mismatches: 41, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
19 20 0.07
20 178 0.67
21 64 0.24
22 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (20 bp):
AATCGCAATGCGATTTACGT
Found at i:11091 original size:21 final size:21
Alignment explanation
Indices: 11063--11137 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
11053 ATTTACGTAA
11063 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* * *
11084 TTGCATTGCG-TTTACGTAA-
1 TCGCATTGCGATTTTCCTAAT
11103 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
11124 TCGCATTGCGATTT
1 TCGCATTGCGATTT
11138 ACGTAATCTC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 9 0.20
20 14 0.30
21 23 0.50
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:11189 original size:21 final size:21
Alignment explanation
Indices: 11164--11216 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
11154 ATTTAAGTAT
*
11164 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
* * *
11185 TCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAAA
11206 TCGCAATGCGA
1 TCGCAATGCGA
11217 TAGTCAGAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:11189 original size:61 final size:61
Alignment explanation
Indices: 11061--11189 Score: 134
Period size: 61 Copynumber: 2.1 Consensus size: 61
11051 TGATTTACGT
* * * * * *
11061 AATCGCATTGCGATTTTCCTAATTTGCATTGCGTTTACGTAATCGCATTGCGATTTTCCTA
1 AATCGCATTGCGATTTACCTAATCTGCATTGCGTTTAAGTAATCGCATTGCGAATTACCAA
* * * * **
11122 ATTCGCATTGCGATTTACGTAATCT-CATTGTGATTTAAGTATTCGCATTGCGAATTAGGAA
1 AATCGCATTGCGATTTACCTAATCTGCATTGCG-TTTAAGTAATCGCATTGCGAATTACCAA
11183 AATCGCA
1 AATCGCA
11190 ACGCGAATTT
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
60 6 0.11
61 48 0.89
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (61 bp):
AATCGCATTGCGATTTACCTAATCTGCATTGCGTTTAAGTAATCGCATTGCGAATTACCAA
Found at i:16231 original size:26 final size:26
Alignment explanation
Indices: 16195--16248 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
16185 ACCGAAGTGC
*
16195 TAATACACATAATGTCATGCCCACCA
1 TAATACACATAAGGTCATGCCCACCA
*
16221 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACATAAGGTCATGCCCACCA
16247 TA
1 TA
16249 TGTACTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.22
Consensus pattern (26 bp):
TAATACACATAAGGTCATGCCCACCA
Found at i:23707 original size:21 final size:20
Alignment explanation
Indices: 23649--23708 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
23639 ATTTTGGTGC
23649 AGAGGGAATCGATCCCCCCA
1 AGAGGGAATCGATCCCCCCA
*
23669 TGAGGGAA-CTGATTCCCCCCA
1 AGAGGGAATC-GA-TCCCCCCA
23690 CAG-GGGAATCGATACCCCC
1 -AGAGGGAATCGAT-CCCCC
23709 TAGGGTTCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
19 1 0.03
20 10 0.30
21 20 0.61
22 2 0.06
ACGTcount: A:0.27, C:0.35, G:0.25, T:0.13
Consensus pattern (20 bp):
AGAGGGAATCGATCCCCCCA
Found at i:31056 original size:43 final size:43
Alignment explanation
Indices: 30982--31186 Score: 272
Period size: 43 Copynumber: 4.8 Consensus size: 43
30972 AGGTCTTATA
* * * *
30982 CTTGCACATAGCAAAAGAGCCT-GGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
*
31024 CTTGCACACATCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
* * *
31067 CTTACACACAGGAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
* * *
31110 CTTGTACACAACAAAAGG-ACCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGC-AAAGGAACCTGGGGGAACTGTAAGGCTTACC
*
31153 CTTGCACACAGCAAAGGGACCT-GGGGAACTGTAA
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAA
31187 CGGTAATTAA
Statistics
Matches: 143, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
42 34 0.24
43 104 0.73
44 5 0.03
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (43 bp):
CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
Found at i:35397 original size:2 final size:2
Alignment explanation
Indices: 35385--35416 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
35375 AAGCATGTGT
*
35385 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35417 GGACAATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:37520 original size:60 final size:59
Alignment explanation
Indices: 37447--37566 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 59
37437 ACACAACTGG
*
37447 TCCCCCGACTATAA-GA-TAATGCTTTATTGAGT-CTCTTGACTATTAAATGTTACAAAATGA
1 TCCCCCGACTATAAGGAGT--TGCTTTATTGAGTAC-CTTGACTATTAAAAGTTAC-AAATGA
*
37507 TCCCCCGACTATAAGGAGTTGCTTTGTTGAGTACCTTGACTATTAAAAGTTACAAATGA
1 TCCCCCGACTATAAGGAGTTGCTTTATTGAGTACCTTGACTATTAAAAGTTACAAATGA
37566 T
1 T
37567 TACTCGACTA
Statistics
Matches: 55, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
59 7 0.13
60 44 0.80
61 3 0.05
62 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (59 bp):
TCCCCCGACTATAAGGAGTTGCTTTATTGAGTACCTTGACTATTAAAAGTTACAAATGA
Found at i:51183 original size:22 final size:22
Alignment explanation
Indices: 51103--51187 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 22
51093 TATTTTCTAC
*
51103 TATCAGTGTTAAGGCACTTTAG
1 TATCAGTGCTAAGGCACTTTAG
* * *
51125 TATTAGTGCGAATGCACTTTCA-
1 TATCAGTGCTAAGGCACTTT-AG
* * * *
51147 TACCAGTGTTGAGGCTCTTTAG
1 TATCAGTGCTAAGGCACTTTAG
51169 TATCAGTGCTAAGGCACTT
1 TATCAGTGCTAAGGCACTT
51188 CTGTTATTCG
Statistics
Matches: 46, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
21 1 0.02
22 44 0.96
23 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (22 bp):
TATCAGTGCTAAGGCACTTTAG
Found at i:51339 original size:115 final size:115
Alignment explanation
Indices: 51137--51369 Score: 387
Period size: 115 Copynumber: 2.0 Consensus size: 115
51127 TTAGTGCGAA
* * * *
51137 TGCACTTTCATACCAGTGTTGAGGCTCTTTAGTATCAGTGCTAAGGCACTTCTGTTATTCGTTGG
1 TGCACTTTCATACCAGTGCTAAGGCTCTTTAGTATCAGTCCTAAGGAACTTCTGTTATTCGTTGG
*
51202 CAAGGCCACGATATATGTATATATAGTAATATACTCACACATTGTGTTTG
66 CAAGGCCACGATATATGTATATATAGTAATATACTCACAAATTGTGTTTG
* *
51252 TGCACTTTCATACCAGTGCTAAGG-TAGTTTAGTATCAGTCCTAAGGAACTTTTGTTATTCGTTG
1 TGCACTTTCATACCAGTGCTAAGGCT-CTTTAGTATCAGTCCTAAGGAACTTCTGTTATTCGTTG
51316 GCAAGGCCACGATATATGTATATATAGTAATATACTCACAAATTGTGTTTG
65 GCAAGGCCACGATATATGTATATATAGTAATATACTCACAAATTGTGTTTG
51367 TGC
1 TGC
51370 TTGATACTTT
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
114 1 0.01
115 109 0.99
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (115 bp):
TGCACTTTCATACCAGTGCTAAGGCTCTTTAGTATCAGTCCTAAGGAACTTCTGTTATTCGTTGG
CAAGGCCACGATATATGTATATATAGTAATATACTCACAAATTGTGTTTG
Found at i:57527 original size:20 final size:20
Alignment explanation
Indices: 57453--57527 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
57443 CCAGAACCCC
* * *
57453 ATGGGGGTATCGATTCCCCT
1 ATGGGGGAATCGGTTCCCTT
**
57473 ACAGGGGAATCGGTTCCCATT
1 ATGGGGGAATCGGTTCCC-TT
*
57494 AAAAGGGGGAATCGGTTCCCTT
1 --ATGGGGGAATCGGTTCCCTT
*
57516 ATGGGGGTATCG
1 ATGGGGGAATCG
57528 ATTACCTCTG
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 24 0.56
21 1 0.02
22 2 0.05
23 16 0.37
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.25
Consensus pattern (20 bp):
ATGGGGGAATCGGTTCCCTT
Found at i:65186 original size:90 final size:89
Alignment explanation
Indices: 65007--65186 Score: 290
Period size: 89 Copynumber: 2.0 Consensus size: 89
64997 CACCCTCACT
*
65007 TCATATTGCACCAATATGAGTAAAAAATAAAATACAAAAGAGATAGGGTGAAAATGCTCCCGTTC
1 TCATATTGCACCAATATGAGCAAAAAATAAAATACAAAAGAGATAGGGTGAAAATGCTCCCGTTC
65072 AATGACGACCAATCGAAACTTAAA
66 AATGACGACCAATCGAAACTTAAA
* *
65096 TCATATTGTC-CCAATATGAGCGAAAAATAAAATGCAAAAGAGATAGGGTGAAAATGCTCGCCGT
1 TCATATTG-CACCAATATGAGCAAAAAATAAAATACAAAAGAGATAGGGTGAAAATGCTC-CCGT
**
65160 TCAATGACGACCGGTCGAAACTTAAA
64 TCAATGACGACCAATCGAAACTTAAA
65186 T
1 T
65187 GATGGTGATG
Statistics
Matches: 84, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
89 54 0.64
90 30 0.36
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (89 bp):
TCATATTGCACCAATATGAGCAAAAAATAAAATACAAAAGAGATAGGGTGAAAATGCTCCCGTTC
AATGACGACCAATCGAAACTTAAA
Found at i:66001 original size:15 final size:15
Alignment explanation
Indices: 65981--66013 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
65971 AACAGAGTAT
65981 ATAAAAATCAAAA-AA
1 ATAAAAA-CAAAATAA
65996 ATAAAAACAAAATAA
1 ATAAAAACAAAATAA
66011 ATA
1 ATA
66014 TTCGATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (15 bp):
ATAAAAACAAAATAA
Found at i:70483 original size:29 final size:30
Alignment explanation
Indices: 70447--70513 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
70437 AGATGAATTT
* *
70447 CTTTATTTCAGGATTATAACTTCAA-TTAG
1 CTTTATTTCAGGATTATAACATCAAGGTAG
* *
70476 CTTTATTTCAGGTTTCTAACATCAAGGTAG
1 CTTTATTTCAGGATTATAACATCAAGGTAG
70506 -TTTATTTC
1 CTTTATTTC
70514 TAGTCCTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 30 0.91
30 3 0.09
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (30 bp):
CTTTATTTCAGGATTATAACATCAAGGTAG
Found at i:73254 original size:19 final size:19
Alignment explanation
Indices: 73230--73267 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
73220 TAGAGGTAAG
73230 TAGATAGG-TGAGGCATACA
1 TAGATAGGTTGAGG-ATACA
73249 TAGATAGGTTGAGGATACA
1 TAGATAGGTTGAGGATACA
73268 ATATTCTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.37, C:0.08, G:0.32, T:0.24
Consensus pattern (19 bp):
TAGATAGGTTGAGGATACA
Found at i:78472 original size:55 final size:55
Alignment explanation
Indices: 78385--78724 Score: 384
Period size: 55 Copynumber: 6.2 Consensus size: 55
78375 CTATGTGTAT
* * *
78385 TATCGACAATAAGAT-TGCAAAACCACGGAATTCATAATATGTTTATGAATGACCG
1 TATCGACACTAAG-TGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
** *
78440 TATCGACACTAAGTGTGCAAAACCATAAAATTCATAATATGTTTATGAAC-ATCCA
1 TATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGA-CCG
* * *
78495 TATCGGA-AATAAGTTTGTAAAACCACGAAATTCATAATATGTTTATGAACGACCG
1 TATC-GACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
* * * * * * * *
78550 TATCGGCACTGAGTGTGCAAAACCACAAAATTCAAAATATATTAATTAACGACTG
1 TATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
* * ** *
78605 TATCGACACTTAGTGTGC-AACCCATTAAATTCATTATATGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
* * * *
78659 TATTGACACTAAGTGTGC-AACCCATGGAATTCATAATATGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
78713 TATCGACACTAA
1 TATCGACACTAA
78725 TTATGAACCC
Statistics
Matches: 240, Mismatches: 40, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
54 90 0.38
55 147 0.61
56 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (55 bp):
TATCGACACTAAGTGTGCAAAACCACGAAATTCATAATATGTTTATGAACGACCG
Found at i:88092 original size:16 final size:15
Alignment explanation
Indices: 88065--88105 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
88055 AAGATGAAAT
88065 AAGAAGAAATGAAGAA
1 AAGAA-AAATGAAGAA
88081 GAAGAAAAATGAAGAA
1 -AAGAAAAATGAAGAA
*
88097 AAGATAAAT
1 AAGAAAAAT
88106 ATGATGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.35
16 10 0.43
17 5 0.22
ACGTcount: A:0.68, C:0.00, G:0.22, T:0.10
Consensus pattern (15 bp):
AAGAAAAATGAAGAA
Found at i:93434 original size:5 final size:5
Alignment explanation
Indices: 93418--93465 Score: 57
Period size: 5 Copynumber: 10.0 Consensus size: 5
93408 GCAAGCACTC
*
93418 AAAAG -AAA- AAAAG AAAAAA AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
93466 TTGAAAGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 10 0.27
5 23 0.62
6 4 0.11
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:93438 original size:10 final size:10
Alignment explanation
Indices: 93418--93464 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 10
93408 GCAAGCACTC
93418 AAAAGAAAAA
1 AAAAGAAAAA
*
93428 AAGA-AAAAA
1 AAAAGAAAAA
*
93437 AAAAGAAAAG
1 AAAAGAAAAA
93447 AAAAG-AAAA
1 AAAAGAAAAA
*
93456 GAAAGAAAA
1 AAAAGAAAA
93465 GTTGAAAGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 15 0.50
10 15 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:93439 original size:11 final size:11
Alignment explanation
Indices: 93423--93455 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
93413 CACTCAAAAG
93423 AAAAAAAGAAA
1 AAAAAAAGAAA
93434 AAAAAAAG-AA
1 AAAAAAAGAAA
*
93444 AAGAAAAGAAA
1 AAAAAAAGAAA
93455 A
1 A
93456 GAAAGAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:93442 original size:19 final size:19
Alignment explanation
Indices: 93418--93465 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
93408 GCAAGCACTC
93418 AAAAGAAAA-AAAGAAAAAA
1 AAAAGAAAAGAAA-AAAAAA
*
93437 AAAAGAAAAGAAAAGAAAA
1 AAAAGAAAAGAAAAAAAAA
*
93456 GAAAGAAAAG
1 AAAAGAAAAG
93466 TTGAAAGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 23 0.88
20 3 0.12
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAGAAAAAAAAA
Found at i:102205 original size:48 final size:48
Alignment explanation
Indices: 102134--102241 Score: 198
Period size: 48 Copynumber: 2.2 Consensus size: 48
102124 GATGGCCATG
102134 CTCCAAAGAAAATGTTACATGGCTGCCACCATTGAGTTCTTCACCCTA
1 CTCCAAAGAAAATGTTACATGGCTGCCACCATTGAGTTCTTCACCCTA
* *
102182 CTCCAAAGAAAATGTTACATGGCTGCCACCGTTGAGTTCTTCGCCCTA
1 CTCCAAAGAAAATGTTACATGGCTGCCACCATTGAGTTCTTCACCCTA
102230 CTCCAAAGAAAA
1 CTCCAAAGAAAA
102242 CCCGACCAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.25
Consensus pattern (48 bp):
CTCCAAAGAAAATGTTACATGGCTGCCACCATTGAGTTCTTCACCCTA
Found at i:103908 original size:20 final size:20
Alignment explanation
Indices: 103879--103917 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
103869 AGAGCTCATA
*
103879 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
103899 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
103918 GTGGAGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:112481 original size:14 final size:13
Alignment explanation
Indices: 112460--112497 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
112450 TGAAGGCTTG
112460 GAGAAGAAAAGAA
1 GAGAAGAAAAGAA
112473 GATGAAGAAAA-AA
1 GA-GAAGAAAAGAA
112486 GAGAAGACAAAG
1 GAGAAGA-AAAG
112498 GTGGAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 5 0.23
13 9 0.41
14 8 0.36
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.03
Consensus pattern (13 bp):
GAGAAGAAAAGAA
Found at i:112933 original size:35 final size:35
Alignment explanation
Indices: 112882--112952 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
112872 ATTATACTAA
* * *
112882 AATACTTATCTATTATTTATCCATAATATTGATTG
1 AATACTTATCTATTATTAATCCATAAAACTGATTG
* *
112917 AATATTTATCTATTATTAATCTATAAAACTGATTG
1 AATACTTATCTATTATTAATCCATAAAACTGATTG
112952 A
1 A
112953 GTTCGATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (35 bp):
AATACTTATCTATTATTAATCCATAAAACTGATTG
Found at i:128010 original size:22 final size:22
Alignment explanation
Indices: 127985--128042 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
127975 CAATACTTAG
* *
127985 AAAAATATCGATATCACAAACC
1 AAAAGTATCGATACCACAAACC
128007 AAAAGTATCGATACCACAAACC
1 AAAAGTATCGATACCACAAACC
*
128029 AAAAGTATCAATAC
1 AAAAGTATCGATAC
128043 TAGCCCTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.53, C:0.22, G:0.07, T:0.17
Consensus pattern (22 bp):
AAAAGTATCGATACCACAAACC
Found at i:137366 original size:10 final size:10
Alignment explanation
Indices: 137351--137395 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
137341 TATGTTAGTA
137351 TATATATTAT
1 TATATATTAT
137361 TATATATTAAT
1 TATATATT-AT
*
137372 ATATAAATTAT
1 -TATATATTAT
*
137383 TATATATTTT
1 TATATATTAT
137393 TAT
1 TAT
137396 TACAAATGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 19 0.63
11 4 0.13
12 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TATATATTAT
Found at i:137381 original size:22 final size:22
Alignment explanation
Indices: 137349--137390 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
137339 GTTATGTTAG
*
137349 TATATATATTATTATATATTAA
1 TATATAAATTATTATATATTAA
137371 TATATAAATTATTATATATT
1 TATATAAATTATTATATATT
137391 TTTATTACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATATAAATTATTATATATTAA
Found at i:145265 original size:22 final size:22
Alignment explanation
Indices: 145237--145282 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
145227 ATTCTGTAAG
*
145237 GATGATAGATTCTCTTTTAAAA
1 GATGATAAATTCTCTTTTAAAA
*
145259 GATGATAAATTCTCTTTTCAAA
1 GATGATAAATTCTCTTTTAAAA
145281 GA
1 GA
145283 CGAAAGCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (22 bp):
GATGATAAATTCTCTTTTAAAA
Found at i:145900 original size:20 final size:20
Alignment explanation
Indices: 145872--146000 Score: 150
Period size: 20 Copynumber: 6.5 Consensus size: 20
145862 CATGAATATT
* * *
145872 TAAAGCCTTCGAGTCATTTG
1 TAAATCCTTCGGGTAATTTG
* *
145892 TAAATCCTTCGAGTCATTTG
1 TAAATCCTTCGGGTAATTTG
* *
145912 TAAATCTTTCGGGTCATTTG
1 TAAATCCTTCGGGTAATTTG
*
145932 TAAAACCTTCGGGTAATTTG
1 TAAATCCTTCGGGTAATTTG
*
145952 TAAAGCCTTCGGGTAATTTG
1 TAAATCCTTCGGGTAATTTG
* * *
145972 AAAAACCTTCGGGAAATTTG
1 TAAATCCTTCGGGTAATTTG
145992 TAAATCCTT
1 TAAATCCTT
146001 TGGGCCATCT
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 97 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (20 bp):
TAAATCCTTCGGGTAATTTG
Found at i:145929 original size:40 final size:40
Alignment explanation
Indices: 145872--146000 Score: 168
Period size: 40 Copynumber: 3.2 Consensus size: 40
145862 CATGAATATT
* * * * *
145872 TAAAGCCTTCGAGTCATTTGTAAATCCTTCGAGTCATTTG
1 TAAATCCTTCGGGTCATTTGTAAAACCTTCGGGTAATTTG
*
145912 TAAATCTTTCGGGTCATTTGTAAAACCTTCGGGTAATTTG
1 TAAATCCTTCGGGTCATTTGTAAAACCTTCGGGTAATTTG
* * * *
145952 TAAAGCCTTCGGGTAATTTGAAAAACCTTCGGGAAATTTG
1 TAAATCCTTCGGGTCATTTGTAAAACCTTCGGGTAATTTG
145992 TAAATCCTT
1 TAAATCCTT
146001 TGGGCCATCT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (40 bp):
TAAATCCTTCGGGTCATTTGTAAAACCTTCGGGTAATTTG
Found at i:146548 original size:10 final size:10
Alignment explanation
Indices: 146530--146574 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
146520 TATGTTAGTA
146530 TATATATTAT
1 TATATATTAT
*
146540 TATACATTAAT
1 TATATATT-AT
*
146551 ATATAAATTAT
1 -TATATATTAT
146562 TATATATTAT
1 TATATATTAT
146572 TAT
1 TAT
146575 TACAAATGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 19 0.63
11 4 0.13
12 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (10 bp):
TATATATTAT
Found at i:146560 original size:22 final size:22
Alignment explanation
Indices: 146528--146570 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
146518 GTTATGTTAG
*
146528 TATATATATTATTATACATTAA
1 TATATAAATTATTATACATTAA
*
146550 TATATAAATTATTATATATTA
1 TATATAAATTATTATACATTA
146571 TTATTACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATAAATTATTATACATTAA
Found at i:151014 original size:23 final size:23
Alignment explanation
Indices: 150982--151033 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
150972 GTACAAGAAG
*
150982 AAAACCACCATAAGAATGAATCA
1 AAAACTACCATAAGAATGAATCA
* *
151005 AAAACTACCATAAGAATTAATCG
1 AAAACTACCATAAGAATGAATCA
151028 AAAACT
1 AAAACT
151034 TTAACCCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.56, C:0.19, G:0.08, T:0.17
Consensus pattern (23 bp):
AAAACTACCATAAGAATGAATCA
Found at i:151318 original size:27 final size:27
Alignment explanation
Indices: 151280--151346 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
151270 CGGTTGGATG
151280 TTGAACCTGGAAGCCAAATCAACAACT
1 TTGAACCTGGAAGCCAAATCAACAACT
151307 TTGAACCTGGAAGCCAAATCAACAACT
1 TTGAACCTGGAAGCCAAATCAACAACT
151334 TTGAACCTGGAAG
1 TTGAACCTGGAAG
151347 TCCCAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (27 bp):
TTGAACCTGGAAGCCAAATCAACAACT
Found at i:153908 original size:14 final size:14
Alignment explanation
Indices: 153872--153909 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
153862 CAGGTCGAGC
*
153872 TGAGTCAACTCACT
1 TGAGTCAACTCAAT
*
153886 T-ATTCAACTCAAT
1 TGAGTCAACTCAAT
153899 TGAGTCAACTC
1 TGAGTCAACTC
153910 GTTAACTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (14 bp):
TGAGTCAACTCAAT
Found at i:157065 original size:27 final size:27
Alignment explanation
Indices: 157035--157090 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
157025 ACCTCGGATT
157035 GGATCGGGTCACCCACATCGGTCTAAG
1 GGATCGGGTCACCCACATCGGTCTAAG
157062 GGATCGGGTCACCCACATCGGTCTAAG
1 GGATCGGGTCACCCACATCGGTCTAAG
157089 GG
1 GG
157091 TTTTACATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.29, G:0.32, T:0.18
Consensus pattern (27 bp):
GGATCGGGTCACCCACATCGGTCTAAG
Found at i:157126 original size:21 final size:21
Alignment explanation
Indices: 157102--157149 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
157092 TTTACATGGA
*
157102 TTACCAAGAAAATTCCATGTC
1 TTACCAAGAAAATTCCATATC
*
157123 TTACCAAGGAAATTCCATATC
1 TTACCAAGAAAATTCCATATC
157144 TTACCA
1 TTACCA
157150 TATATTTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.29
Consensus pattern (21 bp):
TTACCAAGAAAATTCCATATC
Found at i:158792 original size:91 final size:92
Alignment explanation
Indices: 158636--158810 Score: 298
Period size: 91 Copynumber: 1.9 Consensus size: 92
158626 ATGTATTAAC
* * *
158636 ATAGATTCTTTTAAATGTGTTTTTATTTTATTTAAAAGTTAAATATTTCGTTAGCAATCTCTTGA
1 ATAGATTCTTTTAAATATGTTTTTATTTTATTTAAAAGTTAAATATGTCGTTAACAATCTCTTGA
*
158701 GCAAATTGTTAAAAGTTTTCGGTTGGA
66 GCAAATTGTTAAAAATTTTCGGTTGGA
*
158728 ATAGATTC-TTTAAATATGTTTTTATTTTATTTACAAGTTAAATATGTCGTTAACAATCTCTTGA
1 ATAGATTCTTTTAAATATGTTTTTATTTTATTTAAAAGTTAAATATGTCGTTAACAATCTCTTGA
158792 GCAAATTGTTAAAAATTTT
66 GCAAATTGTTAAAAATTTT
158811 TGGATTGAAA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 70 0.90
92 8 0.10
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.47
Consensus pattern (92 bp):
ATAGATTCTTTTAAATATGTTTTTATTTTATTTAAAAGTTAAATATGTCGTTAACAATCTCTTGA
GCAAATTGTTAAAAATTTTCGGTTGGA
Found at i:164642 original size:19 final size:19
Alignment explanation
Indices: 164618--164668 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
164608 TATTTGTACT
*
164618 CTCTCTCTCTCTCACCCCC
1 CTCTCTCTCTCTCACACCC
164637 CTCTCTCTCTCTCACACCC
1 CTCTCTCTCTCTCACACCC
164656 CTCTCTCTCTCTC
1 CTCTCTCTCTCTC
164669 TATAGCTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.06, C:0.59, G:0.00, T:0.35
Consensus pattern (19 bp):
CTCTCTCTCTCTCACACCC
Found at i:164642 original size:21 final size:21
Alignment explanation
Indices: 164616--164669 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
164606 TCTATTTGTA
*
164616 CTCTCTCTCTCTCTCACCCCC
1 CTCTCTCTCTCTCACACCCCC
*
164637 CTCTCTCTCTCTCACACCCCT
1 CTCTCTCTCTCTCACACCCCC
164658 CTCTCTCTCTCT
1 CTCTCTCTCTCT
164670 ATAGCTGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.06, C:0.57, G:0.00, T:0.37
Consensus pattern (21 bp):
CTCTCTCTCTCTCACACCCCC
Found at i:182258 original size:10 final size:10
Alignment explanation
Indices: 182239--182280 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
182229 GTTTTTTGGG
*
182239 TTAAAATATA
1 TTAAATTATA
182249 TTAAATTATA
1 TTAAATTATA
182259 --AAA-TATA
1 TTAAATTATA
182266 TTAAATTATA
1 TTAAATTATA
182276 TTAAA
1 TTAAA
182281 ATTAGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
7 4 0.14
8 3 0.11
9 3 0.11
10 18 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TTAAATTATA
Found at i:182262 original size:17 final size:17
Alignment explanation
Indices: 182240--182275 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
182230 TTTTTTGGGT
182240 TAAAATATATTAAATTA
1 TAAAATATATTAAATTA
182257 TAAAATATATTAAATTA
1 TAAAATATATTAAATTA
182274 TA
1 TA
182276 TTAAAATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATATATTAAATTA
Found at i:182334 original size:18 final size:18
Alignment explanation
Indices: 182303--182348 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
182293 ATTATATTTT
*
182303 TTTTTTGTAATTTTTTGGA
1 TTTTTT-TATTTTTTTGGA
**
182322 TTTTTTTATTTTTTTTTA
1 TTTTTTTATTTTTTTGGA
182340 TTTTTTTAT
1 TTTTTTTAT
182349 ATCTGTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTTTTATTTTTTTGGA
Found at i:182346 original size:10 final size:10
Alignment explanation
Indices: 182322--182346 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
182312 ATTTTTTGGA
182322 TTTTTTTATT
1 TTTTTTTATT
182332 TTTTTTTATT
1 TTTTTTTATT
182342 TTTTT
1 TTTTT
182347 ATATCTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:182382 original size:16 final size:16
Alignment explanation
Indices: 182357--182390 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
182347 ATATCTGTAA
182357 AATTAATATTAT-AAT
1 AATTAATATTATGAAT
182372 AATTAAATATTATGAAT
1 AATT-AATATTATGAAT
182389 AA
1 AA
182391 AGTAGAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTAATATTATGAAT
Found at i:182852 original size:7 final size:7
Alignment explanation
Indices: 182840--182896 Score: 98
Period size: 7 Copynumber: 8.3 Consensus size: 7
182830 TATCCTAAAT
182840 TTTTATA
1 TTTTATA
182847 TTTTATA
1 TTTTATA
182854 TTTTATA
1 TTTTATA
182861 TTTTATA
1 TTTTATA
182868 -TTTATA
1 TTTTATA
182874 TTTTATA
1 TTTTATA
182881 TTTTATA
1 TTTTATA
*
182888 TTTTGTA
1 TTTTATA
182895 TT
1 TT
182897 GATAATTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
6 6 0.12
7 42 0.88
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (7 bp):
TTTTATA
Found at i:182859 original size:27 final size:27
Alignment explanation
Indices: 182829--182887 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
182819 TTTGTATAAA
* *
182829 TTATCCTAAATTTTTATATTTTATATT
1 TTATACTAAATATTTATATTTTATATT
* **
182856 TTATATTTTATATTTATATTTTATATT
1 TTATACTAAATATTTATATTTTATATT
182883 TTATA
1 TTATA
182888 TTTTGTATTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (27 bp):
TTATACTAAATATTTATATTTTATATT
Found at i:182888 original size:27 final size:27
Alignment explanation
Indices: 182841--182905 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
182831 ATCCTAAATT
182841 TTTATATTTTATATTTTATATTTTATA
1 TTTATATTTTATATTTTATATTTTATA
*
182868 TTTATATTTTATATTTTATATTTTGTA
1 TTTATATTTTATATTTTATATTTTATA
*
182895 TTGATAATTTT
1 TTTAT-ATTTT
182906 TCTTCGTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 30 0.86
28 5 0.14
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (27 bp):
TTTATATTTTATATTTTATATTTTATA
Found at i:184157 original size:24 final size:24
Alignment explanation
Indices: 184130--184179 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
184120 TGGTGGTTGA
*
184130 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
184154 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
184178 TT
1 TT
184180 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:193106 original size:24 final size:24
Alignment explanation
Indices: 193074--193123 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
193064 TGGTGGTTGA
*
193074 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
193098 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
193122 TT
1 TT
193124 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:195462 original size:21 final size:22
Alignment explanation
Indices: 195436--195487 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
195426 AGAATAAAAA
195436 ATAATAATATAATAC-TATAAT
1 ATAATAATATAATACATATAAT
*
195457 ATAAT-ATAT-GTACAATATAAT
1 ATAATAATATAATAC-ATATAAT
195478 AT-ATAATATA
1 ATAATAATATA
195488 TAAATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 3 0.12
20 6 0.23
21 17 0.65
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
ATAATAATATAATACATATAAT
Found at i:195513 original size:27 final size:25
Alignment explanation
Indices: 195478--195529 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
195468 ACAATATAAT
195478 ATATAATATATAAATATTTTCAAAATG
1 ATATAATATAT--ATATTTTCAAAATG
195505 ATATAATATATATATTTTCAAAATG
1 ATATAATATATATATTTTCAAAATG
195530 TTTTCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 14 0.56
27 11 0.44
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (25 bp):
ATATAATATATATATTTTCAAAATG
Found at i:195554 original size:37 final size:37
Alignment explanation
Indices: 195505--195676 Score: 283
Period size: 37 Copynumber: 4.6 Consensus size: 37
195495 TTTCAAAATG
*
195505 ATATAATATATATATTTTCAAAATGTTTTCAAAAACT
1 ATATATTATATATATTTTCAAAATGTTTTCAAAAACT
* *
195542 ATATATTATATATATTTTTTCAAAATGTTTTGAAAAATT
1 ATATATTATATATA--TTTTCAAAATGTTTTCAAAAACT
*
195581 ATATAATATATATATTTTCAAAATGTTTTC-AAAACT
1 ATATATTATATATATTTTCAAAATGTTTTCAAAAACT
195617 ATATATTATATATATTTTCAAAATGTTTTCAAAAACT
1 ATATATTATATATATTTTCAAAATGTTTTCAAAAACT
195654 ATATATTATATATATTTTCAAAA
1 ATATATTATATATATTTTCAAAA
195677 ACCGATTTTT
Statistics
Matches: 125, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
36 34 0.27
37 57 0.46
39 34 0.27
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (37 bp):
ATATATTATATATATTTTCAAAATGTTTTCAAAAACT
Found at i:195716 original size:112 final size:105
Alignment explanation
Indices: 195489--195711 Score: 247
Period size: 112 Copynumber: 2.0 Consensus size: 105
195479 TATAATATAT
195489 AAATATTTTCAAAA-TGATATAATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATAT
1 AAAT-TTTTCAAAACT-ATATAATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATAT
* * *
195553 ATATTTTTTCAAAATGTTTTGAAAAATTATATAATATATATATTTTCA
64 ATA-TTTTTCAAAACGTTTT-----ATTATATAAAAAATATATTTTCA
*
195601 AAATGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATA
1 AAAT-TTTTCAAAACTATATAATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATA
*
195666 TA-TTTTCAAAAACCGATTTT-TT-TTTAAAAAACTATATGTTTCA
65 TATTTTTC-AAAA-CG-TTTTATTATATAAAAAA-TATAT-TTTCA
195709 AAA
1 AAA
195712 AAAATCTTTC
Statistics
Matches: 99, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
106 6 0.06
107 7 0.07
108 8 0.08
110 5 0.05
111 4 0.04
112 64 0.65
113 5 0.05
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (105 bp):
AAATTTTTCAAAACTATATAATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATAT
ATTTTTCAAAACGTTTTATTATATAAAAAATATATTTTCA
Found at i:197761 original size:16 final size:16
Alignment explanation
Indices: 197740--197771 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
197730 AACCAATAAT
197740 CAAAGAATCGCAACAA
1 CAAAGAATCGCAACAA
197756 CAAAGAATCGCAACAA
1 CAAAGAATCGCAACAA
197772 GAAACAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CAAAGAATCGCAACAA
Found at i:199696 original size:4 final size:4
Alignment explanation
Indices: 199687--199716 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
199677 ATTTAATTCA
199687 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
199717 GAGAGATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:203949 original size:43 final size:42
Alignment explanation
Indices: 203900--203991 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 42
203890 GTTTTTTTAC
*
203900 TACAAATGCCACTAGTAACTAGGTATTTAGTGGCATTTGTCTT
1 TACAAATGCCACTAGTAACTAAGTATTTAGTGGCATTTGT-TT
* * * *
203943 TACAAATGTCGCTATTGACTAAGTATTTAGTGGCATTTGTTT
1 TACAAATGCCACTAGTAACTAAGTATTTAGTGGCATTTGTTT
203985 TCACAAA
1 T-ACAAA
203992 GGCTGCAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 3 0.07
43 40 0.93
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (42 bp):
TACAAATGCCACTAGTAACTAAGTATTTAGTGGCATTTGTTT
Found at i:205873 original size:6 final size:6
Alignment explanation
Indices: 205864--205907 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
205854 TTTTATTAAG
205864 TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TT
1 TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TT
205908 ATAGAGAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTGCT
Found at i:207977 original size:17 final size:17
Alignment explanation
Indices: 207957--208011 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
207947 ATATATTTGT
207957 AATTTTAATTGAATATA
1 AATTTTAATTGAATATA
* *
207974 AATTCATAAAT-AATATTCA
1 AATT-TTAATTGAATA-T-A
207993 AATTTTAATTGAATATA
1 AATTTTAATTGAATATA
208010 AA
1 AA
208012 ATCTCAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
17 11 0.37
18 10 0.33
19 9 0.30
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (17 bp):
AATTTTAATTGAATATA
Found at i:208004 original size:36 final size:38
Alignment explanation
Indices: 207928--208011 Score: 120
Period size: 36 Copynumber: 2.3 Consensus size: 38
207918 GTATTATAAA
**
207928 TGAATATAAATTCATGATAATATATTTGTAATTTTAAT
1 TGAATATAAATTCATGATAATATATTTCAAATTTTAAT
207966 TGAATATAAATTCAT-A-AATA-ATATTCAAATTTTAAT
1 TGAATATAAATTCATGATAATATAT-TTCAAATTTTAAT
208002 TGAATATAAA
1 TGAATATAAA
208012 ATCTCAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 2 0.05
36 25 0.58
37 1 0.02
38 15 0.35
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (38 bp):
TGAATATAAATTCATGATAATATATTTCAAATTTTAAT
Found at i:208007 original size:19 final size:18
Alignment explanation
Indices: 207957--208013 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
207947 ATATATTTGT
207957 AATTTTAATTGAATA-TA
1 AATTTTAATTGAATATTA
* *
207974 AATTCATAAAT-AATATTCA
1 AATT-TTAATTGAATATT-A
*
207993 AATTTTAATTGAATATAA
1 AATTTTAATTGAATATTA
208011 AAT
1 AAT
208014 CTCAAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
17 8 0.26
18 13 0.42
19 10 0.32
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (18 bp):
AATTTTAATTGAATATTA
Found at i:208226 original size:37 final size:37
Alignment explanation
Indices: 208185--208571 Score: 376
Period size: 37 Copynumber: 11.0 Consensus size: 37
208175 TTTCAAAAAC
*
208185 ATATATATAATATATAGTTTTTAAAAATATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
*
208222 ATATATATAATATATAGTTTTTG--AAT-TTTTTAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
* * * * *
208256 ATATATAT-ATATATA-TATAT--ATATA-TAT--AT
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
* *
208286 ATATATAT-A-ATATAGTTTCTGTAAATATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
* ** *
208321 ATATATATAACATATAGTTTTTGAATTTTTTTTTGAAAA
1 ATATATATAATATATAGTTTTTGAA-AATATTTTG-AAA
* *
208360 TATATATATAATATATAGTTTTTGAAAACATTTTAAAA
1 -ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
208398 AGTATATATAA-ATATA------G----T-TTTTGAAA
1 A-TATATATAATATATAGTTTTTGAAAATATTTTGAAA
* *
208424 ATATATATAATATATAGTTTTTGAAAACATTTTAAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
208461 ATATATATAA-ATATAGTTTTTGAAAATATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
*
208497 ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
*
208534 ATATATATAATATATAAG-TTTTGAAAATATTTTTAAA
1 ATATATATAATATAT-AGTTTTTGAAAATATTTTGAAA
208571 A
1 A
208572 CATTTTAATG
Statistics
Matches: 290, Mismatches: 32, Indels: 56
0.77 0.08 0.15
Matches are distributed among these distances:
25 9 0.03
26 13 0.04
29 5 0.02
30 13 0.04
31 1 0.00
32 12 0.04
33 9 0.03
34 15 0.05
35 12 0.04
36 35 0.12
37 115 0.40
38 20 0.07
39 7 0.02
40 24 0.08
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.46
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
Found at i:208261 original size:2 final size:2
Alignment explanation
Indices: 208256--208299 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
208246 ATTTTTTAAA
208256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
208297 AT A
1 AT A
208300 GTTTCTGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:208301 original size:99 final size:100
Alignment explanation
Indices: 208185--208555 Score: 306
Period size: 103 Copynumber: 3.6 Consensus size: 100
208175 TTTCAAAAAC
208185 ATATATATAATATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATAGTTTTTGAA-TT
1 ATATATAT-A-ATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATAGTTTTTGAATTT
*
208249 TTTTAAAATATATATATATATATATATATATATATAT
64 TTTTAAAATATATATATATATATATATATATATATAA
* ** *
208286 ATATATATAATATAGTTTCTGTAAATATTTTGAAAATATATATAACATATAGTTTTTGAATTTTT
1 ATATATATAATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATAGTTTTTGAA--TTT
*
208351 TTTTGAAAATATATATATA-ATATATAGT-T-TTTGA-AA
64 TTTT-AAAATATATATATATATATATA-TATATAT-ATAA
* * * * *
208387 ACAT-TTTAA-AAAGTATATATAAATATAGTTTTTGAAAATATATATAATATATAGTTTTTGAAA
1 ATATATATAATATAGT-T-TTTAAAAATA--TTTTGAAAATATATATAATATATAGTTTTTG--A
** * * * * * *
208450 ACATTTTAAAAATATATATAAATATAGTTTTTGAAAATATTTTGAAA
60 ATTTTTTTAAAATATATATATATATA-TATAT--ATATA-TAT--AA
* *
208497 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATATAAGTTTT
1 ATATATAT-A-ATATAGTTTTTAAAAATATTTTGAAAATATATATAATATAT-AGTTTT
208556 GAAAATATTT
Statistics
Matches: 213, Mismatches: 30, Indels: 44
0.74 0.10 0.15
Matches are distributed among these distances:
99 51 0.24
100 6 0.03
101 20 0.09
102 28 0.13
103 53 0.25
104 2 0.01
105 2 0.01
107 1 0.00
108 1 0.00
110 28 0.13
111 8 0.04
112 7 0.03
113 2 0.01
114 4 0.02
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (100 bp):
ATATATATAATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATAGTTTTTGAATTTTT
TTAAAATATATATATATATATATATATATATATAA
Found at i:208365 original size:101 final size:96
Alignment explanation
Indices: 208185--208376 Score: 278
Period size: 99 Copynumber: 1.9 Consensus size: 96
208175 TTTCAAAAAC
* *
208185 ATATATATAATATATAGTTTTTAAAAATATTTTGAAAATATATATAATATATAGTTTTTGAATTT
1 ATATATATAATATATAGTTTCTAAAAATATTTTGAAAATATATATAACATATAGTTTTTGAATTT
208250 TTTAAAATATATATATATATATATATATATAT
66 TTTAAAATATATATATATA-ATATATATATAT
**
208282 ATATATATATATAATATAGTTTCTGTAAATATTTTGAAAATATATATAACATATAGTTTTTGAAT
1 ATATATATA-AT-ATATAGTTTCTAAAAATATTTTGAAAATATATATAACATATAGTTTTTGAA-
*
208347 TTTTTTTTGAAA-ATATATATATAATATATA
63 --TTTTTTAAAATATATATATATAATATATA
208377 GTTTTTGAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
97 9 0.11
98 2 0.02
99 47 0.55
100 7 0.08
101 11 0.13
102 9 0.11
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (96 bp):
ATATATATAATATATAGTTTCTAAAAATATTTTGAAAATATATATAACATATAGTTTTTGAATTT
TTTAAAATATATATATATAATATATATATAT
Found at i:208424 original size:26 final size:26
Alignment explanation
Indices: 208390--208523 Score: 97
Period size: 26 Copynumber: 5.3 Consensus size: 26
208380 TTTGAAAACA
*
208390 TTTTAAAAAGTATATATAA-ATATAGT
1 TTTTGAAAA-TATATATAATATATAGT
208416 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGT
* * *
208442 TTTTGAAAACAT-TTTAA-AAATA-T
1 TTTTGAAAATATATATAATATATAGT
* * * *
208465 ATAT-AAATATAGTTTTTGAA-A-ATA--
1 TTTTGAAA-ATA-TATAT-AATATATAGT
208489 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGT
208515 TTTTGAAAA
1 TTTTGAAAA
208524 CATTTTGAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
22 5 0.06
23 9 0.10
24 13 0.15
25 22 0.25
26 38 0.44
ACGTcount: A:0.48, C:0.01, G:0.07, T:0.44
Consensus pattern (26 bp):
TTTTGAAAATATATATAATATATAGT
Found at i:208446 original size:63 final size:62
Alignment explanation
Indices: 208350--208563 Score: 268
Period size: 73 Copynumber: 3.2 Consensus size: 62
208340 TTTGAATTTT
208350 TTTTTGAAAATATATATATAATATATAGTTTTTGAAAACATTTTAAAAAGTATATATAAATATAG
1 TTTTTG-AAA-ATATATATAATATATAGTTTTTGAAAACATTTTAAAAA-TATATATAAATATAG
208415 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAAATATAGTTT
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAAATATA----
208480 TTG
62 --G
*
208483 AAAATATTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATATA
1 ----T-TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAA-ATA
208548 TAAG
60 T-AG
208552 -TTTTGAAAATAT
1 TTTTTGAAAATAT
208564 TTTTAAAACA
Statistics
Matches: 135, Mismatches: 1, Indels: 28
0.82 0.01 0.17
Matches are distributed among these distances:
62 14 0.10
63 50 0.37
64 3 0.02
65 6 0.04
68 1 0.01
69 1 0.01
72 1 0.01
73 54 0.40
74 4 0.03
75 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.44
Consensus pattern (62 bp):
TTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAAATATAG
Found at i:208494 original size:11 final size:11
Alignment explanation
Indices: 208442--208577 Score: 53
Period size: 11 Copynumber: 11.4 Consensus size: 11
208432 AATATATAGT
*
208442 TTTTGAAAACA
1 TTTTGAAAATA
*
208453 TTTTAAAAATA
1 TTTTGAAAATA
*
208464 TATAT-AAATATA
1 T-TTTGAAA-ATA
208476 GTTTTTGAAAATA
1 --TTTTGAAAATA
208489 TTTTGAAAATA
1 TTTTGAAAATA
*
208500 TATAT-AATATATA
1 T-TTTGAA-A-ATA
*
208513 GTTTTTGAAAACA
1 --TTTTGAAAATA
208526 TTTTGAAAATA
1 TTTTGAAAATA
*
208537 TATAT-AATATATAA
1 T-TTTGAA-A-AT-A
208551 GTTTTGAAAATA
1 -TTTTGAAAATA
* *
208563 TTTTTAAAACA
1 TTTTGAAAATA
208574 TTTT
1 TTTT
208578 AATGTATTAT
Statistics
Matches: 96, Mismatches: 12, Indels: 34
0.68 0.08 0.24
Matches are distributed among these distances:
11 53 0.55
12 12 0.12
13 14 0.15
14 11 0.11
15 6 0.06
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:208614 original size:29 final size:30
Alignment explanation
Indices: 208573--208630 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
208563 TTTTTAAAAC
*
208573 ATTTTAATGTATTA-TATTTTATATTTTAT
1 ATTTTAATATATTATTATTTTATATTTTAT
* *
208602 ATTTTATTATATTATTATTTTATTTTTTA
1 ATTTTAATATATTATTATTTTATATTTTA
208631 GTTTCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (30 bp):
ATTTTAATATATTATTATTTTATATTTTAT
Found at i:208646 original size:7 final size:7
Alignment explanation
Indices: 208584--208630 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
208574 TTTTAATGTA
208584 TTATATT
1 TTATATT
208591 TTATATT
1 TTATATT
208598 TTATATT
1 TTATATT
*
208605 TTATTATA
1 TTA-TATT
208613 TTATTATT
1 TTA-TATT
*
208621 TTATTTT
1 TTATATT
208628 TTA
1 TTA
208631 GTTTCTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
7 23 0.64
8 13 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTATATT
Found at i:210055 original size:2 final size:2
Alignment explanation
Indices: 210048--210096 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
210038 TCTCGACATG
210048 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
210090 TA TA TA T
1 TA TA TA T
210097 GCTTTGTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:211761 original size:16 final size:16
Alignment explanation
Indices: 211740--211770 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
211730 AAGGACAAAA
211740 TAGTGGTTATATTTAG
1 TAGTGGTTATATTTAG
211756 TAGTGGTTATATTTA
1 TAGTGGTTATATTTA
211771 AACCCACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (16 bp):
TAGTGGTTATATTTAG
Found at i:220099 original size:18 final size:18
Alignment explanation
Indices: 220075--220125 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
220065 GAGGGTTCAT
*
220075 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAA
* * *
220093 TGTGGTCATTTGGGACAA
1 AGTGGTCCTTCGGGACAA
220111 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
220126 TAAATTTTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAA
Found at i:225999 original size:35 final size:35
Alignment explanation
Indices: 225948--226018 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
225938 ATTTTTCTTA
*
225948 TTTCTTTTGAACTCAATTTTTTTTCATTAAGTACT
1 TTTCTTTTGAACTCAATTTTCTTTCATTAAGTACT
* * *
225983 TTTCTTTTGAATTCAATTTTCTTTCGTTCAGTACT
1 TTTCTTTTGAACTCAATTTTCTTTCATTAAGTACT
226018 T
1 T
226019 CATTTTATCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.58
Consensus pattern (35 bp):
TTTCTTTTGAACTCAATTTTCTTTCATTAAGTACT
Found at i:229567 original size:45 final size:45
Alignment explanation
Indices: 229512--229597 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
229502 AATATTTCTC
* *
229512 TTAGGTTGAAAACACAAAAGGGCGCCCTAAGTTGAAAAAAATCAT
1 TTAGGGTGAAAACACAAAAGGGCGCCCTAAATTGAAAAAAATCAT
* * *
229557 TTAGGGTGAAAACCCGAAAGGGCGCCTTAAATTGAAAAAAA
1 TTAGGGTGAAAACACAAAAGGGCGCCCTAAATTGAAAAAAA
229598 ATGGGTCCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (45 bp):
TTAGGGTGAAAACACAAAAGGGCGCCCTAAATTGAAAAAAATCAT
Found at i:231205 original size:39 final size:39
Alignment explanation
Indices: 231138--231467 Score: 407
Period size: 39 Copynumber: 8.4 Consensus size: 39
231128 GTTTGTTAAA
* * *
231138 AAAACATTTTGAAAATATATATATATAATATGTAGTTTTTA
1 AAAATATTTTG-AAA-ATATATATATAATATATAGTTTTTG
* * *
231179 AAAATATTTTCAATATATATATATAATATGTAGTTTTTTG
1 AAAATATTTTGAAAATATATATATAATATATAG-TTTTTG
* *
231219 AAAACATTTTAAAAATATATATATATAATATATAGTTTTTG
1 AAAATATTTT-GAAA-ATATATATATAATATATAGTTTTTG
*
231260 AAAATATTTTG-AAA-ATATATATAACATATAGTTTTTG
1 AAAATATTTTGAAAATATATATATAATATATAGTTTTTG
* *
231297 AAAATGTTTTGAAAAAATATATATAATATATAGTTTTTG
1 AAAATATTTTGAAAATATATATATAATATATAGTTTTTG
* *
231336 AAAACATTTTAAAAAATATATATATAATATATAGTTTTTG
1 AAAATATTTT-GAAAATATATATATAATATATAGTTTTTG
*
231376 AAAATATTTTGAAAAAATATATATAATATATAGTTTTTG
1 AAAATATTTTGAAAATATATATATAATATATAGTTTTTG
* * *
231415 AAAACATTTTG-AAA-ATATATATAATATATAATTTTTAA
1 AAAATATTTTGAAAATATATATATAATATATAGTTTTT-G
*
231453 AAAATATTTTTAAAA
1 AAAATATTTTGAAAA
231468 CATTTTCATG
Statistics
Matches: 256, Mismatches: 25, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
37 53 0.21
38 16 0.06
39 91 0.36
40 52 0.20
41 26 0.10
42 18 0.07
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (39 bp):
AAAATATTTTGAAAATATATATATAATATATAGTTTTTG
Found at i:231244 original size:118 final size:117
Alignment explanation
Indices: 231138--231450 Score: 413
Period size: 116 Copynumber: 2.6 Consensus size: 117
231128 GTTTGTTAAA
* * *
231138 AAAACATTTTGAAAATATATATATATAATATGTAGTTTTTAAAAATATTTTCAATATATATATAT
1 AAAATATTTTGAAAATATATATATATAATAT-TAGTTTTTGAAAATATTTTGAA-A-ATATATAT
* *
231203 AATATGTAGTTTTTTGAAAACATTTTAAAAATATATATATATAATATATAGTTTTTG
63 AATATATAGTTTTTTGAAAACATTTTAAAAA-ATATATATAT-ATATATTGTTTTTG
* *
231260 AAAATATTTTGAAAATATATATA-A-CATA-TAGTTTTTGAAAATGTTTTGAAAAAATATATATA
1 AAAATATTTTGAAAATATATATATATAATATTAGTTTTTGAAAATATTTTG--AAAATATATATA
*
231322 ATATATAG-TTTTTGAAAACATTTTAAAAAATATATATATAATATATAGTTTTTG
64 ATATATAGTTTTTTGAAAACATTTTAAAAAATATATATAT-ATATATTGTTTTTG
*
231376 AAAATATTTTGAAAA-A-ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAA
1 AAAATATTTTGAAAATATATATATATAATAT-TAGTTTTTGAAAATATTTTGAAAATATATATAA
*
231439 TATATAATTTTT
65 TATATAGTTTTT
231451 AAAAAATATT
Statistics
Matches: 174, Mismatches: 10, Indels: 19
0.86 0.05 0.09
Matches are distributed among these distances:
114 5 0.03
115 2 0.01
116 62 0.36
117 25 0.14
118 51 0.29
119 1 0.01
120 5 0.03
121 1 0.01
122 22 0.13
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (117 bp):
AAAATATTTTGAAAATATATATATATAATATTAGTTTTTGAAAATATTTTGAAAATATATATAAT
ATATAGTTTTTTGAAAACATTTTAAAAAATATATATATATATATTGTTTTTG
Found at i:231467 original size:118 final size:117
Alignment explanation
Indices: 231138--231455 Score: 462
Period size: 118 Copynumber: 2.7 Consensus size: 117
231128 GTTTGTTAAA
* * * *
231138 AAAACATTTTGAAAATATATATATATAATATGTAGTTTTTAAAAATATTTTCAATATATATATAT
1 AAAATATTTTGAAAA-A-ATATATATAATATATAGTTTTTGAAAATATTTTGAA-A-ATATATAT
*
231203 AATATGTAGTTTTTTGAAAACATTTTAAAAATATATATATATAATATATAGTTTTTG
62 AATATATAG-TTTTTGAAAACATTTTAAAAATATATATATATAATATATAGTTTTTG
* *
231260 AAAATATTTTG--AAAATATATATAACATATAGTTTTTGAAAATGTTTTGAAAAAATATATATAA
1 AAAATATTTTGAAAAAATATATATAATATATAGTTTTTGAAAATATTTTG--AAAATATATATAA
231323 TATATAGTTTTTGAAAACATTTTAAAAA-ATATATATATAATATATAGTTTTTG
64 TATATAGTTTTTGAAAACATTTTAAAAATATATATATATAATATATAGTTTTTG
*
231376 AAAATATTTTGAAAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATAATA
1 AAAATATTTTGAAAAAATATATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATAATA
* *
231441 TATAATTTTTAAAAA
66 TATAGTTTTTGAAAA
231456 ATATTTTTAA
Statistics
Matches: 180, Mismatches: 12, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
116 64 0.36
117 21 0.12
118 79 0.44
119 2 0.01
120 4 0.02
122 10 0.06
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.44
Consensus pattern (117 bp):
AAAATATTTTGAAAAAATATATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATAATA
TATAGTTTTTGAAAACATTTTAAAAATATATATATATAATATATAGTTTTTG
Found at i:231485 original size:79 final size:77
Alignment explanation
Indices: 231138--231467 Score: 430
Period size: 79 Copynumber: 4.2 Consensus size: 77
231128 GTTTGTTAAA
* * * * *
231138 AAAACATTTTGAAAATATATATATATAATATGTAGTTTTTAAAAATATTTTCAATATATATATAT
1 AAAATATTTTGAAAA-A-ATATATATAATATATAGTTTTTGAAAACATTTTGAA-ATATATATAT
*
231203 AATATGTAGTTTTTTG
63 AATATATAG-TTTTTG
* * *
231219 AAAACATTTTAAAAATATATATATATAATATATAGTTTTTGAAAATATTTTGAAA-ATATATATA
1 AAAATATTTTGAAAA-A-ATATATATAATATATAGTTTTTGAAAACATTTTGAAATATATATATA
*
231283 ACATATAGTTTTTG
64 ATATATAGTTTTTG
* *
231297 AAAATGTTTTGAAAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAAATATATATATA
1 AAAATATTTTGAAAAAATATATATAATATATAGTTTTTGAAAACATTTT--GAAATATATATATA
231362 ATATATAGTTTTTG
64 ATATATAGTTTTTG
231376 AAAATATTTTGAAAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAA-ATATATATAAT
1 AAAATATTTTGAAAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAATATATATATAAT
* *
231440 ATATAATTTTTAA
66 ATATAGTTTTT-G
*
231453 AAAATATTTTTAAAA
1 AAAATATTTTGAAAA
231468 CATTTTCATG
Statistics
Matches: 228, Mismatches: 17, Indels: 12
0.89 0.07 0.05
Matches are distributed among these distances:
76 53 0.23
77 18 0.08
78 21 0.09
79 85 0.37
80 1 0.00
81 50 0.22
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (77 bp):
AAAATATTTTGAAAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAATATATATATAAT
ATATAGTTTTTG
Found at i:238271 original size:26 final size:26
Alignment explanation
Indices: 238224--238322 Score: 84
Period size: 26 Copynumber: 3.9 Consensus size: 26
238214 ATATAAAAGA
*
238224 TTTTTA-TATGTAGTAAGTGTGTGTATT
1 TTTTTATTATGCAGTAA--GTGTGTATT
238251 TTTTTATTATGCAGTAAGTGTGTA-T
1 TTTTTATTATGCAGTAAGTGTGTATT
** *
238276 TTAATATATATTCA-T--GTGTGT-TCT
1 TTTTTAT-TATGCAGTAAGTGTGTAT-T
238300 TTTTTATTATGCAGTAAGTGTGT
1 TTTTTATTATGCAGTAAGTGTGT
238323 GTATTTAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
23 11 0.19
24 7 0.12
25 7 0.12
26 18 0.31
27 6 0.10
28 9 0.16
ACGTcount: A:0.23, C:0.04, G:0.19, T:0.54
Consensus pattern (26 bp):
TTTTTATTATGCAGTAAGTGTGTATT
Found at i:238303 original size:49 final size:49
Alignment explanation
Indices: 238241--238436 Score: 208
Period size: 54 Copynumber: 4.0 Consensus size: 49
238231 ATGTAGTAAG
238241 TGTGTGTAT-TTTTTTATTATGCAGTAAGTGTGTATTTAATATATATTCA
1 TGTGTGTATCTTTTTTATTATGCAGTAAGTGTGTATTTAATATATATT-A
238290 TGTGTGT-TCTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATATTTA
1 TGTGTGTATCTTTTTTATTATGCAGTAA--GTGTGTATTTAATATATA-TTA
* *
238341 TGTGTGTATGCTTTTTTTATTATGCAGTATGTGTGTGTGTTTAATATATATGTA
1 TGTGTGTAT-C-TTTTTTATTATGCAGTA--AGTGTGTATTTAATATATAT-TA
* * * *
238395 TGTGTG---C--TTTTATTATGCAATACGTGTGTGTTTAATGTATAT
1 TGTGTGTATCTTTTTTATTATGCAGTAAGTGTGTATTTAATATATAT
238437 ATGAAATGTG
Statistics
Matches: 132, Mismatches: 5, Indels: 24
0.82 0.03 0.15
Matches are distributed among these distances:
45 18 0.14
47 14 0.11
48 1 0.01
49 25 0.19
50 1 0.01
51 26 0.20
52 3 0.02
53 2 0.02
54 42 0.32
ACGTcount: A:0.23, C:0.05, G:0.19, T:0.53
Consensus pattern (49 bp):
TGTGTGTATCTTTTTTATTATGCAGTAAGTGTGTATTTAATATATATTA
Found at i:238323 original size:51 final size:51
Alignment explanation
Indices: 238241--238400 Score: 229
Period size: 54 Copynumber: 3.1 Consensus size: 51
238231 ATGTAGTAAG
238241 TGTGTGTAT-TTTTTTATTATGCAGTAA--GTGTGTATTTAATATATATTCA
1 TGTGTGTATCTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATATT-A
238290 TGTGTGT-TCTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATATTTA
1 TGTGTGTATCTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATA-TTA
* *
238341 TGTGTGTATGCTTTTTTTATTATGCAGTATGTGTGTGTGTTTAATATATATGTA
1 TGTGTGTAT-C-TTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATAT-TA
238395 TGTGTG
1 TGTGTG
238401 CTTTTATTAT
Statistics
Matches: 101, Mismatches: 2, Indels: 11
0.89 0.02 0.10
Matches are distributed among these distances:
48 1 0.01
49 25 0.25
51 26 0.26
52 3 0.03
53 2 0.02
54 44 0.44
ACGTcount: A:0.23, C:0.04, G:0.20, T:0.54
Consensus pattern (51 bp):
TGTGTGTATCTTTTTTATTATGCAGTAAGTGTGTGTATTTAATATATATTA
Found at i:238520 original size:54 final size:50
Alignment explanation
Indices: 238435--238552 Score: 148
Period size: 54 Copynumber: 2.3 Consensus size: 50
238425 TTTAATGTAT
238435 ATATGAAATGTGTGTGAATGATTATAATATAAAGGGTGTGTGCTCTT-TTA
1 ATATGAAATGTGTGTGAATGATTATAATATAAAGGGTGTGTG-TCTTGTTA
* * *
238485 TTATGAAATGTGTGTGAGTGAGTTTTTATAATATAAAGGGTGTGTGTGTTGTTA
1 ATATGAAATGTGTGTGAATGA----TTATAATATAAAGGGTGTGTGTCTTGTTA
*
238539 ATGTGAAATGTGTG
1 ATATGAAATGTGTG
238553 AGTTTTTATA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
50 19 0.33
53 3 0.05
54 36 0.62
ACGTcount: A:0.29, C:0.02, G:0.28, T:0.42
Consensus pattern (50 bp):
ATATGAAATGTGTGTGAATGATTATAATATAAAGGGTGTGTGTCTTGTTA
Found at i:238527 original size:28 final size:27
Alignment explanation
Indices: 238456--238528 Score: 64
Period size: 28 Copynumber: 2.7 Consensus size: 27
238446 GTGTGAATGA
238456 TTATAATATAAAGGGTGT-GTGCTCTT
1 TTATAATATAAAGGGTGTGGTGCTCTT
* *
238482 TTAT--TATGAAATGTGTGTGAGTGAGT-TT
1 TTATAATAT-AAA-GGGTGTG-GTG-CTCTT
238510 TTATAATATAAAGGGTGTG
1 TTATAATATAAAGGGTGTG
238529 TGTGTTGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
24 3 0.08
25 3 0.08
26 9 0.24
28 15 0.41
29 4 0.11
30 3 0.08
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.42
Consensus pattern (27 bp):
TTATAATATAAAGGGTGTGGTGCTCTT
Found at i:238574 original size:24 final size:24
Alignment explanation
Indices: 238502--238576 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
238492 ATGTGTGTGA
*
238502 GTGAGTTTTTATAATATAAAGG-GT
1 GTGAGTTTTTATAATAT-GAGGTGT
* * * **
238526 GTGTGTGTTGT-TAATGTGAAATGT
1 GTGAGT-TTTTATAATATGAGGTGT
238550 GTGAGTTTTTATAATATGAGGTGT
1 GTGAGTTTTTATAATATGAGGTGT
238574 GTG
1 GTG
238577 TTTTCGAAAG
Statistics
Matches: 37, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
23 4 0.11
24 30 0.81
25 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (24 bp):
GTGAGTTTTTATAATATGAGGTGT
Found at i:240501 original size:15 final size:15
Alignment explanation
Indices: 240481--240522 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
240471 ACTTCATGGG
*
240481 TAAGAAGACAACATC
1 TAAGAAGAAAACATC
*
240496 TAAGAAGAAAACATA
1 TAAGAAGAAAACATC
*
240511 AAAGAAGAAAAC
1 TAAGAAGAAAAC
240523 GTCACAGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.64, C:0.12, G:0.14, T:0.10
Consensus pattern (15 bp):
TAAGAAGAAAACATC
Found at i:249047 original size:21 final size:21
Alignment explanation
Indices: 249013--249062 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
249003 CAATCAGAAC
*
249013 AAAAAGGA-CAAAAACA-AAAA
1 AAAAAGAAGCAAAAA-AGAAAA
249033 AGAAAAGAAGCAAAAAAGAAAA
1 A-AAAAGAAGCAAAAAAGAAAA
249055 AAAAAGAA
1 AAAAAGAA
249063 AGAACAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 14 0.54
22 11 0.42
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (21 bp):
AAAAAGAAGCAAAAAAGAAAA
Found at i:249064 original size:14 final size:14
Alignment explanation
Indices: 249010--249085 Score: 64
Period size: 16 Copynumber: 5.0 Consensus size: 14
249000 ATTCAATCAG
*
249010 AACAAAAAGGACAAA
1 AACAAAAA-GAAAAA
249025 AACAAAAAAGAAAAGA
1 AAC-AAAAAGAAAA-A
*
249041 AGCAAAAAAGAAAAA
1 AAC-AAAAAGAAAAA
249056 AA-AAGAAAGAACAAA
1 AACAA-AAAGAA-AAA
249071 AATCAAAAAGAAAAA
1 AA-CAAAAAGAAAAA
249086 GGGACAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 2 0.04
14 6 0.12
15 17 0.33
16 25 0.48
17 2 0.04
ACGTcount: A:0.79, C:0.08, G:0.12, T:0.01
Consensus pattern (14 bp):
AACAAAAAGAAAAA
Found at i:249065 original size:30 final size:30
Alignment explanation
Indices: 249008--249085 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
248998 AGATTCAATC
*
249008 AGAACAAAAAGGACAAAAACAAAAAAGAA-A
1 AGAACAAAAAAGA-AAAAACAAAAAAGAACA
249038 AGAAGCAAAAAAGAAAAAA-AAAGAAAGAACA
1 AGAA-CAAAAAAGAAAAAACAAA-AAAGAACA
*
249069 AAAATC-AAAAAGAAAAA
1 AGAA-CAAAAAAGAAAAA
249086 GGGACAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 3 0.07
30 26 0.62
31 13 0.31
ACGTcount: A:0.78, C:0.08, G:0.13, T:0.01
Consensus pattern (30 bp):
AGAACAAAAAAGAAAAAACAAAAAAGAACA
Found at i:250609 original size:12 final size:12
Alignment explanation
Indices: 250592--250625 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
250582 AAACAACTTC
250592 CCAATTTCAAAG
1 CCAATTTCAAAG
250604 CCAATTTCAAAG
1 CCAATTTCAAAG
250616 CCAATTTCAA
1 CCAATTTCAA
250626 CTTCACAGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.06, T:0.26
Consensus pattern (12 bp):
CCAATTTCAAAG
Found at i:250790 original size:106 final size:106
Alignment explanation
Indices: 250604--252252 Score: 2515
Period size: 106 Copynumber: 15.6 Consensus size: 106
250594 AATTTCAAAG
* * *
250604 CCAATTTCAAAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
*
250669 CTTCACGACGAAGGGACCGCTGATTGTCAACAAACAACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* *
250710 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* * * *
250775 CTTCATGACGAAGGGACCGCTGGTTGTCAATAAATAATTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* *
250816 CCAATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* * * *
250881 CTTCATGACGAAGGGACTGCTGGTTGTCAATAAATAACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* * *
250922 TCAATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
*
250987 CTTCACGAAGAAGGGACCGCTGGTTGTCAACAAACAACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* * * *
251028 CCAATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGGACACGAGACAACGCAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
*
251093 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* * * *
251134 CCAATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACACAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* *
251199 CTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* * * * *
251240 TCAATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCCAGACAATGCAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
*
251305 CTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
*
251346 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* * *
251411 CTTCACGACGAAGGGACTGCTGGTTGTCAATAAATAACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* *
251452 TCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
*
251517 CTTCACGAAGAAGGGACCGCTGGTTGTCAACAAACAACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* * * * *
251558 CCAATTTCATAGCCAATTTCAACTTCACAGCGAATGATATTGGACACGAGACAACGCAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
*
251623 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* * ** *
251664 CCAATTTCGGAGCCAATTTCAACTTCACAGCGAAAAATATTGGACTCCAGACAACACAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* *
251729 CTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* * * *
251770 TCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCCAGACAATGCAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
*
251835 CTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* *
251876 TCATTTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* * *
251941 CTTCACGACGAAGGGACTGCTGGTTGTTAACAAATAACTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* *
251982 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* *
252047 CTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAATTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* * * *
252088 CCAATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* * * *
252153 CTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTC
66 CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
* * * * * * * *
252194 CCGATTCCAGAGCCAATTTCAACTTCACGACGGACGATATTGGCCTCGAAACAACGCAA
1 CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
252253 CTTACATTGG
Statistics
Matches: 1418, Mismatches: 125, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 1418 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
CTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTC
Found at i:255592 original size:20 final size:21
Alignment explanation
Indices: 255562--255612 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
255552 AAAAAGAAAG
*
255562 AAATGGAGGAGG-GAACACCGC
1 AAAT-GAGGAGGAGAACACCAC
* *
255583 AAATGAGGAGGAGAAGAGCAC
1 AAATGAGGAGGAGAACACCAC
255604 AAATGAGGA
1 AAATGAGGA
255613 CAAGGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.45, C:0.12, G:0.37, T:0.06
Consensus pattern (21 bp):
AAATGAGGAGGAGAACACCAC
Found at i:257221 original size:13 final size:13
Alignment explanation
Indices: 257203--257232 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
257193 AATGACACGC
*
257203 AATGTAAGTCGTA
1 AATGTAAGTCATA
257216 AATGTAAGTCATA
1 AATGTAAGTCATA
257229 AATG
1 AATG
257233 CGTGTCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (13 bp):
AATGTAAGTCATA
Found at i:257317 original size:13 final size:13
Alignment explanation
Indices: 257299--257337 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
257289 AATGACGCGC
257299 AATGCGCGTCATA
1 AATGCGCGTCATA
*
257312 AATGCGTGTCATA
1 AATGCGCGTCATA
257325 AATGCGCGTCATA
1 AATGCGCGTCATA
257338 GATTTATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:262347 original size:26 final size:26
Alignment explanation
Indices: 262311--262364 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
262301 ACCGAAGTGC
262311 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACATAAGGTCGTGCCCACCA
*
262337 TAATACACATAAGGTTGTGCCCACCA
1 TAATACACATAAGGTCGTGCCCACCA
262363 TA
1 TA
262365 TGCACTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (26 bp):
TAATACACATAAGGTCGTGCCCACCA
Found at i:271884 original size:2 final size:2
Alignment explanation
Indices: 271877--271904 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
271867 AGTATTCTTA
271877 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
271905 CCTAAATGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:273907 original size:15 final size:15
Alignment explanation
Indices: 273887--273915 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
273877 TTATAAATTT
273887 AATTGGGTCAGGCTC
1 AATTGGGTCAGGCTC
273902 AATTGGGTCAGGCT
1 AATTGGGTCAGGCT
273916 TAGGCCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.28
Consensus pattern (15 bp):
AATTGGGTCAGGCTC
Found at i:274881 original size:15 final size:15
Alignment explanation
Indices: 274861--274889 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
274851 TTATAAATTT
274861 AATTGGGTCAGGCTC
1 AATTGGGTCAGGCTC
274876 AATTGGGTCAGGCT
1 AATTGGGTCAGGCT
274890 TGGGCCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.28
Consensus pattern (15 bp):
AATTGGGTCAGGCTC
Found at i:275461 original size:31 final size:31
Alignment explanation
Indices: 275425--275483 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
275415 AACTTAAAAG
* *
275425 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
275456 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
275484 CAATATAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:275534 original size:22 final size:22
Alignment explanation
Indices: 275508--275550 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
275498 TAATAAATTA
275508 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
275530 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
275551 CTGATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:275559 original size:22 final size:22
Alignment explanation
Indices: 275510--275558 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
275500 ATAAATTATT
**
275510 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATGA
275532 TAAAATAAATCAATCCATACTGA
1 TAAAATAAATCAATCCATA-TGA
275555 TAAA
1 TAAA
275559 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATGA
Found at i:275561 original size:54 final size:54
Alignment explanation
Indices: 275498--276286 Score: 562
Period size: 54 Copynumber: 14.4 Consensus size: 54
275488 ATAACTACAA
275498 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
275552 TGATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAA-TC---C--AT--A-T-TTTAAAATAAATCAATCCATAC
** * ** * ** **
275615 TTTTAAAATAAAT-CAATCCATACTAATAGAT-TATTTAAAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
** * ** * ** **
275669 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
* * *
275724 -AACTACA--A--T--AATATATCAATCCATATTTTAAAATAAATCAATCCATAG
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
275772 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
*
275830 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
275884 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * * * *
275941 TTTTAAA--A--T-AAATCAATCCATACTAATAAATTATATAAAATAAATCAATTCATA-
1 TAATAAATTATTTAAAATAAATCAAT-C-CAT--ATT-T-TAAAATAAATCAATCCATAC
** * *
275995 TTTTAAA--A--T-AAATCAATCCATACCAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAAT-CC-AT--A-T-TTTAAAATAAATCAATCCATAC
*
276050 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
276098 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
276152 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
276206 TAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA----C
276264 TAATAAATTATTTTAAAATAAAT
1 TAATAAATTA-TTTAAAATAAAT
276287 AACCTTATTA
Statistics
Matches: 628, Mismatches: 56, Indels: 97
0.80 0.07 0.12
Matches are distributed among these distances:
48 54 0.09
49 7 0.01
50 8 0.01
51 1 0.00
52 14 0.02
53 8 0.01
54 375 0.60
55 19 0.03
56 1 0.00
57 13 0.02
58 74 0.12
59 12 0.02
60 2 0.00
62 6 0.01
63 11 0.02
64 23 0.04
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:275573 original size:14 final size:14
Alignment explanation
Indices: 275554--275605 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
275544 ATCCATACTG
275554 ATAAATTATTTAAA
1 ATAAATTATTTAAA
* *
275568 ATAAATCAATTCATACTA
1 ATAAAT-TATT--TA-AA
275586 ATAAATTATTTAAA
1 ATAAATTATTTAAA
275600 ATAAAT
1 ATAAAT
275606 CAATCCATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 13 0.43
15 5 0.17
17 5 0.17
18 7 0.23
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAAATTATTTAAA
Found at i:275620 original size:22 final size:22
Alignment explanation
Indices: 275594--275636 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
275584 TAATAAATTA
275594 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
275616 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
275637 CTAATAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:275674 original size:22 final size:22
Alignment explanation
Indices: 275648--275690 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
275638 TAATAGATTA
275648 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
275670 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
275691 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Done.